Publications by authors named "Tom O"

3 Publications

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ToTem: a tool for variant calling pipeline optimization.

BMC Bioinformatics 2018 06 26;19(1):243. Epub 2018 Jun 26.

Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.

Background: High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall.

Results: Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data.

Conclusions: ToTem is a tool for automated pipeline optimization which is freely available as a web application at .
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June 2018

Lipoma of the cheek presenting with recurrent sialadenitis of the right parotid gland: a case report.

J Med Case Rep 2016 Nov 3;10(1):311. Epub 2016 Nov 3.

Department of Oral and Maxillofacial Surgery, Oral Pathology/Medicine and Oral Radiology, University of Nairobi Dental Hospital, P.O. Box 19676-00202, Nairobi, Kenya.

Background: Lipomas are benign neoplasms arising from adipose tissue. Oral lipomas have been reported in the buccal mucosa, tongue, floor of the mouth and lips; however, the case of a lipoma occurring as an antecedent lesion to recurrent sialadenitis is hitherto unreported in the English literature.

Case Presentation: We report the case of an intraoral lipoma occurring with signs and symptoms of recurrent sialadenitis in a 15-year-old Kenyan girl of Kikuyu descent. The lipoma was antecedent leading to partial obstruction and stasis related to the right Stensen's duct culminating in recurrent sialadenitis of the ipsilateral parotid gland. Due to the slow growth, softness, diffuse nature and lack of pain, lipomas may exist below the diagnostic radar, hence, the need to have a high index of suspicion and utilize diagnostic aids as necessary. In this case magnetic resonance imaging was key in establishing the existence of the lipoma. The lipoma was excised with resolution of the recurrent sialadenitis.

Conclusions: The purpose of this report is to present the diagnostic challenge emanating from the pressure effects of an intraoral soft tissue lipoma masquerading as recurrent sialadenitis with a view to improving on patient care through sensitization.
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November 2016

Do computer-generated summaries, "The Bottom Line (TBL)" accurately reflect published journal abstracts?

AMIA Annu Symp Proc 2007 Oct 11:1135. Epub 2007 Oct 11.

Himmelfarb Health Sciences Library, The George Washington University Medicial Center, Washington DC 20037, USA.

txt2MEDLINE allows users to search and retrieve MEDLINE/PubMed citations using SMS text messages. "The Bottom Line" (TBL) concept was developed because of the 160-character limitation of text messages. TBL algorithm generates a shortened version of the published abstract thereby decreasing the number of characters while attempting to maintain the key points of the full-length, author-generated abstract. The data seems to indicate that the TBL generally conveys the essential elements of the full abstract.
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October 2007